Zea mays genome annotation pdf

A genome wide characterization of microrna genes in maize. Zxgdb is being developed as a part of our nsffunded project cyberinfrastructure for comparative plant genome research through plantgdb pi. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results. Pdf genome assembly of a tropical maize inbred line. The genome wide distribution of dna methylation and h3k9me2 were investigated in seedling tissue for the maize inbred b73 and compared to. The leafy stalk of the plant produces pollen inflorescences and separate ovuliferous inflorescences called ears that yield kernels or seeds, which are fruits.

Genomewide association analysis of seedling root development. Our data offer a rich resource for constructing the pan genome of zea mays and genetic improvement of modern maize varieties. We report an improved draft nucleotide sequence of the 2. To further our understanding of how genome and transcriptome variation contribute to the production of highyielding hybrids, we generated a draft genome assembly of the inbred line ph207 to complement and compare with the existing b73 reference. Maranas department of chemical engineering, the pennsylvania state university, university park, pennsylvania, united states of america. The maize oligonucleotide array maizearray is one of the few microarray platforms designed for genome wide gene expression analysis in zea mays l. New lncrna annotation reveals extensive functional divergence. Characterizing the pan genome of maize with pacbio smrt sequencing michelle vierra, greg concepcion, aaron wenger, david rank, paul peluso pacbio, 5 obrien drive, menlo park, ca 94025 improved genome annotation the era of the pangenome7 acknowledgements the authors would like to thank everyone associated with the. Variants segregating above 5% minor allele frequency maf in the union of all lines were considered for mapping. The agpv4 genome, agpv4 annotation, and the michigan state university msu functional annotation is available to download below. Ncbi is actively annotating genes in the version 3 maize genome with comprehensive details of gene structure, neighboring loci, expression.

The refseq genome records for zea mays were annotated by the ncbi eukaryotic genome annotation pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. Shared protocolpreparingarabidopsisdnafor20kbsmrtbelllibraries. Availability of the complete zea mays genome sequence maize inbred line b73 has made it possible for the first time to identify all the lrrcontaining receptorlike genes in this plant species. Zea mays maize has the highest worldwide production of all grain crops, yielding 875 million tonnes in 2012. Many genome projects have annotations that embody years of manual curation and revision. The number of fulllength cdnas from maize zea mays l. The genome annotation and rnaseq coverage can also be viewed in the jbrowse genome browser. Herein, we introduce a genome scale model for a plant with direct applications to food and bioenergy production i. Nevertheless, attempts to engineer plant metabolism for desired overproductions have been met with only limited success 12. The dna binding domain, also named the dof domain, has. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. To further our understanding of how genome and transcriptome variation contribute to the production of highyielding hybrids, we generated a draft genome assembly of the inbred line ph207 to complement and compare with the existing b73. Zea mays maize has historically been used as a model species for genetics, development, physiology and more recently, genome structure. Corn insects and crop genetics research unit and department of genetics, development, and cell biology.

The aim of this study was insilico structural annotation of an amino. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary bac bibac libraries for the maize inbred b73 and the. Maizegdb is a communityoriented, longterm, federally funded informatics service to researchers focused on the crop plant and model organism zea mays. Homologues are provided for several other monocots and arabidopsis thaliana. Automated update, revision and quality control of the zea.

Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary bac. Eukaryotic chromosomes consist of dnaprotein complexes referred to as chromatin. From the first step of nbsfilter, a total of 217 nbsencoding genes were identified in the genomic sequence of maize inbred line b73 and collected. Further information about the species will be included in the title and metadata of the assembly.

Thatcher,a wengang zhou,b april leonard,a bingbing wang,b,c mary beatty,b gina zastrowhayes,b xiangyu zhao,a,d andy baumgarten,b and bailin lia,1 a dupont pioneer, wilmington, delaware 19880 b dupont pioneer, johnston, iowa 501. Apr 29, 2009 our data describe targeted genome modification in zea mays. Transcriptomewide association supplements genomewide. Improved maize reference genome with singlemolecule. Here we report the construction of a fulllength enriched cdna library from osmotically stressed maize seedlings by using the modi. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary bac bibac libraries for the maize inbred b73 and the sorghum landrace nengsi1. Maize was domesticated from wild teosinte in central america and its cultivation spread throughout the americas by precolumbian civilisations.

As an ancient segmental tetraploid, the maize zea mays l. Genomic distribution of h3k9me2 and dna methylation in a. There will be disappointment when the research communities realize that they dont have the gold standard of sequence as present in arabidopsis and rice. The scope and breadth of genome scale metabolic reconstructions have continued to expand over the last decade. Caveats of genome annotationgreatly impacted by the quality of the sequence. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. N early i dentical p aralogs nips are defined as paralogous genes that exhibit. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Praise and stargaze yingjie xiao 1,4, haijun liu, liuji wu2, marilyn warburton3 and jianbing yan1, 1national key laboratory of crop genetic improvement, huazhong agricultural university, wuhan 430070, china. Genomic resources for gene discovery, functional genome.

Dof proteins have two functional domains, a dnabinding domain at the nterminus and a transcriptional regulatory domain at the cterminus 14. Methods we used whole genome sequence data to map regions of zea mays ssp. Gene annotations were updated using 11 fulllength transcripts. Genome wide analysis of alternative splicing in zea mays. Using transcriptome sequencing of seedling rna from 503 maize zea mays inbred lines to characterize the maize pan genome, we identified 8681 representative transcript assemblies rtas1 with 16. Pdf insilico structural annotation of methylthioadenosine.

The mass genome annotation mga repository is a resource designed to store published next generation sequencing data and other genome annotation data such as gene start sites, snps, etc. Automated update, revision and quality control of the zea mays. A comprehensive genome scale metabolic reconstruction of maize metabolism article pdf available in plos one 67. Contributions of zea mays subspecies mexicana haplotypes to. In response we have developed makerp, a fast and easytouse genome annotation engine for plants. Hzs, comparative genomic analysis, tandem duplication. Thiolspecific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively by similarity. Precise genome modification in the crop species zea mays. Zeamap, a comprehensive database adapted to the maize. Our data describe targeted genome modification in zea mays. Pdf maize has a long history of genetic and genomic tool development and is.

Jan 01, 2007 as an ancient segmental tetraploid, the maize zea mays l. In annotation release 101 a total of 47,446 genes were annotated, including 37,380 that code for proteins. Genomewide analysis of alternative splicing in zea mays. Seems to contribute to the inhibition of germination during stress by similarity. Automated update, revision, and quality control of the. Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity.

Although a food staple in many regions of the world, most is used for animal feed and ethanol fuel. Maize is an important model organism for fundamental research into the inheritance and functions of genes, the physical linkage of genes to chromosomes, the mechanistic relation between cytological crossovers. The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of highquality gene structure annotations challenging. The grasses originated 5570 million years ago mya and subsequently diversified to include all the major cereal crop species in addition to nearly. Intense artificial selection over the last 100 years has produced elite maize zea mays inbred lines that combine to produce highyielding hybrids. The huangzaosi maize genome provides insights into. Background the spread of maize cultivation to the highlands of central mexico was accompanied by substantial introgression from the endemic wild teosinte zea mays ssp. The chromatin interaction and histone modification data were. Praise and stargaze yingjie xiao 1,4, haijun liu, liuji wu2, marilyn warburton3 and jianbing yan1, 1national key laboratory of crop genetic improvement, huazhong agricultural university, wuhan 430070, china 2synergetic innovation center of henan grain crops, henan agricultural university, zhengzhou 450002, china. Zea mays, more commonly referred to as maize, is a member of the grass family poaceae, or true grasses. In corn, increasing altitude has been correlated with decreasing knob cbanded heterochromatin, suggesting that dna content may decrease with increasing altitude. A comprehensive genome scale metabolic reconstruction of maize metabolism rajib saha, patrick f.

Additional two letter codes can be used for other species in the genus zea as follows. The counts and characteristics of the annotated features. Understanding of the relationship between chromatin structure and genome behavior is a long term goal of this project nsf 1444532. Maize is thought to have originated 5570 million years ago in what is now central or south america and has since diversified into nearly 10 000 nondomestic relatives. The maize genome is complex with striking intraspecific variation in gene order, repetitive dna content, and allelic content exceeding the levels observed between primate species. N2 previous studies have indicated a positive correlation between genome size and altitude among plant species. It has been hypothesized that increasing genome size occurs due to increasing cbanded heterochromatin. Browse the list download sequence and annotation from refseq or genbank. Letters precise genome modification in the crop species zea mays using zincfinger nucleases vipula k. Zea mays data mapped to agpv4 reference for structural variant. Pdf genetic and genomic toolbox of zea mays researchgate. In response, we have developed makerp, a fast and easytouse genome annotation engine for plants. Dna methylation and dimethylation of lysine 9 of histone h3 h3k9me2 are two chromatin modifications that can be associated with gene expression or recombination rate. Identification of immune related lrrcontaining genes in.

This data is now available for download and can be explored in the genome data viewer, with blast, and in the gene database. Makerp identified and annotated 4,466 additional, wellsupported proteincoding genes not present in. In addition to its agronomic importance, maize has been a keystone model organism for basic research for nearly a century. The genome assembly and annotations of zea mays ssp. Zea mays subspecies mays zm zea mays subspecies parviglumis zv zea mays subspecies mexicana zx zea mays subspecies huehuetenangensis zh.

A reference genome is a haploid representation of a genome as dna sequence with a defined coordinate system, and accession and version identification. Maizegdb is a founding member of agbiodata, a consortuim of agriculturerelated online resources which is committed to making agriculturerelated research data fair. Insights into the maize pangenome and pantranscriptome. The microarray technology has become an established approach for largescale gene expression analysis with mature protocols for sample, microarray, and data processing. Gene annotations were updated using 111,000 fulllength transcripts. Characterization of introgression from the teosinte zea. Contributions of zea mays subspecies mexicana haplotypes.

A blast server is also available for searching your sequences against b73 v2 through v4 genome and annotation. A genome wide analysis of the cellulose synthaselike csl gene family in maize zea mays yongkai li 2 1, xiaojie cheng 1, yaqin fu 1, qinqin wu 1, yuli guo 1, jiayu peng, wei zhang corresp. Zheng58, chang72, and mo17 and maize wild relatives zea mays ssp. The tabs below show categories for template queries, which provide simple search menus. Characterizing the pangenome of maize with pacbio smrt. Previous studies have indicated a positive correlation between genome size and altitude among plant species. This report presents statistics on the annotation products, the input data used in the. Rnasequencing of different b73 tissues were from 9, and rnaseq data of developing maize kernels from 368 amp inbred lines were from 10. Draft assembly of elite inbred line ph207 provides. Zhang l, chia jm, kumari s, stein jc, liu z, narechania a, maher ca, guill k, mcmullen md, ware d. A near complete snapshot of the zea mays seedling transcriptome revealed from ultradeep sequencing.

Zmgdb is being developed as a part of our nsffunded project cyberinfrastructure for comparative plant genome research through plantgdb pi. Reannotation of the maize oligonucleotide array seifert. A new maize zea mays genome annotation has been produced by the refseq eukaryotic genome annotation pipeline. Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. Annotation and expression profile analysis of 2073 full. The purpose of this resource is to provide a convenient sequencecentered genome view for zea mays, with a narrow focus on gene structure annotation. Our immediate aim is to identify and map genome wide changes in chromatin structure using nuclease sensitivity profiling in five diverse tissues of maize. Sep 01, 2019 genotypes for the goodman diversity panel flintgarcia et al. Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Sequence analyses of the gene space of the maize inbred line b73 genome, coupled with wet lab validation, have revealed. Draft assembly of elite inbred line ph207 provides insights. Genomewide analysis of immunophilin fkbp genes and. The maize genome provides a complex landscape of interspersed genes and transposons. Fulllength cdnas are very important for genome annotation and functional analysis of genes.